crossing96/oncoscreening huggingface dataset:
Advanced Age Impacts Survival After Radical Nephroureterectomy for Upper Tract Urothelial Carcinoma.	INTRODUCTION: Upper tract urothelial carcinoma is rare but has a poor prognosis. Prognostic factors have been extensively studied in order to provide the best possible management for patients. We have aimed to investigate commonly available factors predictive of recurrence and survival in this patient population at high risk of death and recurrence, with an emphasis on the effects of age (using a cutoff of 70 years) on survival outcomes. PATIENTS AND METHODS: From 1387 patients with clinically nonmetastatic upper tract urothelial carcinoma treated with radical nephroureterectomy at 21 academic hospital centers between 2005 and 2021, 776 patients were eligible and included in the study. Univariable and multivariable Cox regression models were built to evaluate the independent prognosticators for intravesical and extravesical recurrence, overall survival, and cancer-specific survival according to age groups. A P value of <.05 was considered statistically significant. RESULTS: We did not find an association between groups aged <70 and >70 years old and preoperatively clinical or histopathological characteristics. Kaplan-Meier analysis was found no statistical significance between the 2 age groups in terms of intravesical or extravesical recurrence (P = .09 and P = .57). Overall survival (P = .0001) and cancer-specific survival (P = .0001) have been found to be statistically significantly associated with age as independent predictors (confounding factors: gender, tumor size, tumor side, clinical T stage, localization, preoperative hydronephrosis, tumor localization, type of surgery, multifocality of the tumor, pathological grade, lymphovascular invasion, concomitant CIS, lymph node status, necrosis, or history of previous bladder cancer). CONCLUSION: This research confirms that patients aged 70 and above who undergo radical nephroureterectomy may have worse outcomes compared to younger patients, older patients needing an improved care and management of UTUC to improve their outcomes in the setting of an increase in this aged population group.	bladder
[Antibody-drug conjugates directed against NECTIN-4 as a new treatment option for patients with metastatic urothelial carcinoma].	This compact review article highlights the background and importance of nectins in cancer therapy, focusing specifically on the antibody-drug conjugate enfortumab vedotin (EV) as a targeted treatment option for metastatic urothelial carcinoma. The evolving understanding of nectin-4 expression and its impact on EV therapy underscores the need for personalized approaches to ensure optimal patient outcomes. Further investigation into biomarker-guided therapies and prospective clinical trials are critical to refining patient selection and treatment strategies.	bladder
MRI-based automated machine learning model for preoperative identification of variant histology in muscle-invasive bladder carcinoma.	OBJECTIVES: It is essential yet highly challenging to preoperatively diagnose variant histologies such as urothelial carcinoma with squamous differentiation (UC w/SD) from pure UC in patients with muscle-invasive bladder carcinoma (MIBC), as their treatment strategy varies significantly. We developed a non-invasive automated machine learning (AutoML) model to preoperatively differentiate UC w/SD from pure UC in patients with MIBC. METHODS: A total of 119 MIBC patients who underwent baseline bladder MRI were enrolled in this study, including 38 patients with UC w/SD and 81 patients with pure UC. These patients were randomly assigned to a training set or a test set (3:1). An AutoML model was built from the training set, using 13 selected radiomic features from T2-weighted imaging, semantic features (ADC values), and clinical features (tumor length, tumor stage, lymph node metastasis status), and subsequent ten-fold cross-validation was performed. A test set was used to validate the proposed model. The AUC of the ROC curve was then calculated for the model. RESULTS: This AutoML model enabled robust differentiation of UC w/SD and pure UC in patients with MIBC in both training set (ten-fold cross-validation AUC = 0.955, 95% confidence interval [CI]: 0.944-0.965) and test set (AUC = 0.932, 95% CI: 0.812-1.000). CONCLUSION: The presented AutoML model, that incorporates the radiomic, semantic, and clinical features from baseline MRI, could be useful for preoperative differentiation of UC w/SD and pure UC. CLINICAL RELEVANCE STATEMENT: This MRI-based automated machine learning (AutoML) study provides a non-invasive and low-cost preoperative prediction tool to identify the muscle-invasive bladder cancer patients with variant histology, which may serve as a useful tool for clinical decision-making. KEY POINTS: • It is important to preoperatively diagnose variant histology from urothelial carcinoma in patients with muscle-invasive bladder carcinoma (MIBC), as their treatment strategy varies significantly. • An automated machine learning (AutoML) model based on baseline bladder MRI can identify the variant histology (squamous differentiation) from urothelial carcinoma preoperatively in patients with MIBC. • The developed AutoML model is a non-invasive and low-cost preoperative prediction tool, which may be useful for clinical decision-making.	bladder
Diagnostic accuracy of MUC7 expression for bladder cancer: A systematic review and meta-analysis.	BACKGROUND: There have been many studies on MUC7 and bladder cancer (BC) that have been published; however, all sample sizes were not enough which led to their conclusions being based on small samples. Therefore, this meta-analysis aims to systematically analyze the diagnostic value of MUC7 for bladder cancer and provide a scientific basis for the diagnosis of bladder cancer. METHODS: To obtain relevant literature on MUC7 diagnosed bladder cancer, databases such as PubMed, Web of Science, Cochrane Library, China National Knowledge Infrastructure, Wanfang data, Chongqing VIP, and Chinese Biomedical Literature Database were searched from the establishment of the database to July 11, 2023. According to established inclusion and exclusion criteria, literature was screened and data were extracted. The Quality Assessment of Diagnostic Accuracy Studies 2 was used to evaluate the risk of bias and applicability of included literature. Meta-disc1.4 and Stata12.0 software were used for Meta-analysis. RESULTS: Twelve studies were included, including728 BC patients and 458 non-BC controls. The pooled sensitivity and pooled specificity were 0.74 (95% confidence interval [CI]: 0.71-0.77) and 0.92 (95% CI: 0.90-0.95), respectively. The pooled negative likelihood ratio was 0.27 (95% CI: 0.20-0.36), and the pooled positive likelihood ratio was 9.58 (95% CI: 5.40-17.00). The diagnostic odds ratio was 40.95 (95% CI: 20.31-82.59), and the area under the curve was 0.91 in the overall summary of the receiver operating characteristic curve. CONCLUSION: MUC7 might be a potential biomarker for diagnosing BC. However, more large sample and multicenter studies are needed to prove whether it can be used in clinical diagnosis.	bladder
High grade urothelial carcinoma in kidney transplant patients with a history of BK viremia - Just a coincidence?	INTRODUCTION: Kidney transplant recipients (KTR) have a three-to-four-fold increased risk of developing urothelial carcinoma (UC) compared to the general population. BK polyoma virus (BKV) infection is known to affect approximately 15% of KTR. In vitro models support a potential pathogenic role for BKV in the development of UC. We describe a series of UC in kidney transplant recipients. METHODS: Electronic patient records were searched to identify KTR with UC who had undergone kidney only or simultaneous kidney and pancreas transplantation in a single UK center between 2009 and 2015. Where available, stored pathological samples were retrieved, re-examined and stained for SV40 as a marker of BKV using standard staining protocols for kidney biopsy samples. RESULTS: Fourteen KTR had developed UC post-transplant. Of these, 10 KTR had a history of BKV infection post-transplant. Six of these 10 KTR developed a rare micropapillary tumor subtype of UC which is typically only found in <1% of UC cases. All six micropapillary tumor samples stained positive for SV40, including samples from metastases. Three tumor samples were available from the four KTR with no history of BKV infection and were not micropapillary subtype and were negative for SV40. Three micropapillary tumors from immunocompetent patients were examined as controls and were negative for SV40. CONCLUSIONS: These findings would support a pathogenic role for BK virus in the development of rare micropapillary subtype urothelial tumors in the kidney transplant population.	bladder
Construction of a prediction model for prognosis of bladder cancer based on the expression of ion channel-related genes.	OBJECTIVES: To construct a prediction model for the prognosis of bladder cancer patients based on the expression of ion channel-related genes (ICRGs). METHODS: ICRGs were obtained from the existing researches. The clinical information and the expression of ICRGs mRNA in breast cancer patients were obtained from the Cancer Genome Atlas database. Cox regression analysis, minimum absolute shrinkage and selection operator regression analysis were used to screen breast cancer prognosis related genes, which were verified by immunohistochemistry and qRT-PCR. The risk scoring equation for predicting the prognosis of patients with bladder cancer was constructed, and the patients were divided into high-risk group and low-risk group according to the median risk score. Immune cell infiltration was compared between the two groups. Kaplan-Meier survival curve and receiver operating characteristic (ROC) curve were used to evaluate the accuracy and clinical application value of the risk scoring equation. The factors related to the prognosis of bladder cancer patients were analyzed by univariate and multivariate Cox regression, and a nomogram for predicting the prognosis of bladder cancer patients was constructed. RESULTS: By comparing the expression levels of ICRGs in bladder cancer tissues and normal bladder tissues, 73 differentially expressed ICRGs were dentified, of which 11 were related to the prognosis of bladder cancer patients. Kaplan-Meier survival curve suggested that the risk score based on these 11 genes was negatively correlated with the prognosis of patients. The area under the ROC curve of the risk score for predicting the prognosis of patients at 1, 3 and 5 year was 0.634, 0.665 and 0.712, respectively. Stratified analysis showed that the ICRGs-based risk score performed well in predicting the prognosis of patients with American Joint Committee on Cancer (AJCC) stage Ⅲ-Ⅳ bladder cancer (P<0.05), while it had a poor value in predicting the prognosis of patients with AJCC stage Ⅰ-Ⅱ (P>0.05). There were significant differences in the infiltration of plasma cells, activated natural killer cells, resting mast cells and M2 macrophages between the high-risk group and the low-risk group. Cox regression analysis showed that risk score, smoking, age and AJCC stage were independently associated with the prognosis of patients with bladder cancer (P<0.05). The nomogram constructed by combining risk score and clinical parameters has high accuracy in predicting the 1, 3 and 5 year overall survival rate of bladder cancer patients. CONCLUSIONS: The study shows the potential value of ICRGs in the prognostic risk assessment of bladder cancer patients. The constructed prognostic nomogram based on ICRGs risk score has high accuracy in predicting the prognosis of bladder cancer patients.	bladder
Prognostic Ability of Nutritional Indices for Outcomes of Bladder Cancer: A Systematic Review and Meta-Analysis.	BACKGROUND: Nutrition has become an important parameter influencing the prognosis of several cancers. However, its impact on outcomes for bladder cancer (BC) is still unclear. This review examines the association between three commonly used nutritional indices, namely, the prognostic nutritional index (PNI), controlling nutritional status (CONUT), and the geriatric nutritional risk index (GNRI) and outcomes of BC. METHODS: PubMed, CENTRAL, Scopus, Web of Science, Embase, and Google Scholar were explored for studies published up to April 13, 2023. Data from studies were pooled to examine the association between PNI, CONUT, or GNRI and overall survival (OS) and recurrence-free survival (RFS). RESULTS: Thirteen studies were included. Meta-analysis demonstrated significantly poor OS with low PNI versus high PNI in BC patients (hazard ratio [HR]: 1.71; 95% confidence interval [CI]: 1.37, 2.14; I2 = 0%). This result remained significant in various subgroup analyses. However, no association was noted between PNI and RFS (HR: 1.22; 95% CI: 0.67, 2.24; I2 = 84%). Meta-analysis showed that patients with high CONUT scores had significantly poor OS (HR: 2.43; 95% CI: 1.82, 3.25; I2 = 0%) as well as RFS (HR: 2.90; 95% CI: 2.10, 4.01; I2 = 0%). Data on GNRI were scarce and conflicting. CONCLUSION: Limited data show that PNI and CONUT are predictive of outcomes in BC. Low PNI was associated with poor OS, while high CONUT was associated with poor OS and RFS. Data on GNRI are too scarce to obtain conclusions. Further studies are needed to supplement the results.	bladder
Primary high-grade urothelial carcinoma of prostate with prostatic hyperplasia: a rare case report and review of the literature.	BACKGROUND: Primary urothelial carcinoma in the prostate (UCP) is extremely rare and occurs most frequently in the bladder. There are only dozens of primary cases reported in the literature. Here, we describe a rare case of primary UCP and review the literature. CASE PRESENTATION: A 67-year-old widowed male, was referred to our hospital due to the frequency, and urgency of dysuria. Magnetic resonance imaging (MRI) examination revealed prostate size was about 57 mm × 50 mm × 54 mm, increased prostatic transitional zone, and surrounding of prostatic duct indicate bar isointense T1, short T2, hyperintense DWI, and hyposignal ADC (PI-RADS 3); posterior of peripheral zone indicate patchy isointense T1, short T2, hyperintense DWI, and hyposignal ADC (PI-RADS 5). Subsequently, the patient underwent a transrectal prostate biopsy. Histopathological and immunohistochemical (IHC) assessments showed prostatic high-grade urothelial carcinoma with benign prostatic hyperplasia. Finally, the patient underwent laparoscopic radical prostatectomy. Four months after surgery, CT plain and enhanced scan revealed thickening of the bladder wall. On further workup, cystoscopy revealed lymphoid follicular changes in the cut edge of the radical prostatectomy, and cystoscopic biopsies showed the malignant tumor. CONCLUSIONS: Prostatic urothelial carcinoma should always be considered if the patient with severe lower urinary tract symptoms or hematuria, PSA, and digital rectal examination without abnormalities, without a personal history of urothelial cancer, but contrast-enhanced MRI showed the lesion located in the prostate. As of right now, radical surgical resections remain the most effective treatment. The effectiveness of neoadjuvant or adjuvant chemotherapy is still controversial.	bladder
Oncological effectiveness of bladder-preserving trimodal therapy versus radical cystectomy for the treatment of muscle-invasive bladder cancer: a system review and meta-analysis.	OBJECTIVE: Radical cystectomy (RC) is the gold standard treatment for muscle-invasive bladder cancer (MIBC). As a bladder-preservation option recommended in guidelines, trimodal therapy (TMT) has become increasingly popular in recent years. However, it is still uncertain whether TMT can provide comparable oncologic outcomes to RC. Therefore, it is imperative to evaluate whether TMT yields comparable outcomes to RC. METHODS: We conducted a systematic search of Web of Science, MEDLINE, the Cochrane Library, and EMBASE databases up to June 2023 to identify studies that met our inclusion criteria. The primary outcome measures evaluated in this study were overall survival (OS) and cancer-specific survival (CSS). The study quality was evaluated independently by two authors, and data were extracted accordingly. RESULTS: After excluding duplicates and ineligible articles, our meta-analysis included seven studies involving 3,489 and 13,877 patients in the TMT and RC groups, respectively. Short-term overall survival rates were comparable between the groups, but beyond 5 and > 10-years, the RC group had significantly higher overall survival rates compared to the TMT group. In terms of cancer-specific survival, there was no significant difference between the groups at 1-year follow-up, but from the second year onwards, including the 5-year and > 10-year nodes, the RC group had significantly better outcomes compared to the TMT group. CONCLUSION: The treatment effect of RC is better than that of TMT. Unless the patient can't tolerate RC or has a strong desire to preserve the bladder, RC should be chosen over TMT in treatment, and patients undergoing TMT should be closely followed up.	bladder
Genome-wide exploration of genetic interactions for bladder cancer risk.	Although GWASs have been conducted to investigate genetic variation of bladder tumorigenesis, little is known about genetic interactions that may influence bladder cancer (BC) risk. By leveraging large-scale participants from UK Biobank, we established a discovery database with 4000 Caucasian participants (2000 cases vs 2000 non-cases), a database with 1648 Caucasian participants (824 cases vs 824 non-cases) and 856 non-Caucasian participants (428 cases vs 428 non-cases) as validation. We then performed a genome-wide SNP-SNP interaction investigation related to BC risk based a machine learning approach (ie, GenEpi). Moreover, we used the selected interactions to build a BC screening model with an integrated interaction-empowered polygenic risk score (iPRS) based on Cox proportional hazard model. With Bonferroni correction, we identified 10 statistically significant pairs of SNPs, which located in 17 chromosomes. Of these, four SNP-SNP interactions were found to be positively associated with BC risk among Caucasian participants (ORs 1.57-2.03), while six SNP-SNP interactions showed negatively associated with BC risk (ORs 0.54-0.65). Only four of the SNP-SNP interactions were consistently identified in non-Caucasian participants located in ST7L-ADSS2, FHIT-CHDH, LARP4B-LHPP and RBFOX3-MPRIP. In addition, the iPRS showed a HR of 1.81 (95% CI: 1.46-2.09) compared the highest tertile to the lowest tertile, with an enhanced AUC (0.91; 95% CI:0.85-0.97) than PRS (AUC: 0.86; 95% CI:0.76-0.95; P-(DeLong test)  = 2.2 × 10(-4) ). In summary, this study identified several important SNP-SNP interactions for BC risk, and developed an iPRS model for BC screening, which may help to identify the people at high-risk state of BC before early manifestation.	bladder
Primary mucosal melanomas of the urogenital tract: a clinical, pathological, and genetic nationwide survey of Danish patients 1990-2019.	PURPOSE: To describe the epidemiologic, clinical, histopathological, and genetic features of primary mucosal melanoma of the urinary tract in a national Danish cohort with cases included from the year 1990 to 2019. MATERIAL AND METHODS: Patients of the Danish cohort were found using national databases. Only primary tumours were included in the cohort. Appropriate formalin-fixed paraffin-embedded blocks underwent next-generation sequencing. RESULTS: Eight cases of primary urinary bladder melanomas and 18 cases of primary urethral melanomas were included. Bladder melanomas had an incidence of 0.05 cases/million/year. Mean age at diagnosis was 67 years. The most frequent primary treatment was cystectomy. Adjuvant treatment was given in three cases and consisted of chemotherapy or radiotherapy. Mutations were found in the NF1, KRAS, ATRX, TP53, RAC1, and BRAF genes. Urethral melanomas were found to have an incidence of 0.12 cases/million/year. Average age at diagnosis was 77 years. The most frequent treatment was excision of the tumour. Adjuvant treatment was given in nine cases and most frequently consisted of radiotherapy. Mutations were found in the NF1, TERT PROMOTOR, NRAS, ATRX, TP53, ATM, TSC2, and CREBBP genes. The 5-year survival of patients with bladder melanoma was 12.5% and 22.2% for patients with urethral melanoma. CONCLUSION: Our study highlights the rarity of urinary tract melanomas and their poor prognosis. The most widely used treatment for urogenital mucosal melanoma remains surgical while adjuvant therapy strategies are evolving. Next-generation sequencing showed mutational patterns with no location-specific patterns. The most frequent mutations were in the NF1, ATRX, NRAS, and TP53 genes.	bladder
Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer.	BACKGROUND: In humans, muscle-invasive bladder cancer (MIBC) is highly aggressive and associated with a poor prognosis. With a high mutation load and large number of altered genes, strategies to delineate key driver events are necessary. Dogs and cats develop urothelial carcinoma (UC) with histological and clinical similarities to human MIBC. Cattle that graze on bracken fern also develop UC, associated with exposure to the carcinogen ptaquiloside. These species may represent relevant animal models of spontaneous and carcinogen-induced UC that can provide insight into human MIBC. RESULTS: Whole-exome sequencing of domestic canine (n = 87) and feline (n = 23) UC, and comparative analysis with human MIBC reveals a lower mutation rate in animal cases and the absence of APOBEC mutational signatures. A convergence of driver genes (ARID1A, KDM6A, TP53, FAT1, and NRAS) is discovered, along with common focally amplified and deleted genes involved in regulation of the cell cycle and chromatin remodelling. We identify mismatch repair deficiency in a subset of canine and feline UCs with biallelic inactivation of MSH2. Bovine UC (n = 8) is distinctly different; we identify novel mutational signatures which are recapitulated in vitro in human urinary bladder UC cells treated with bracken fern extracts or purified ptaquiloside. CONCLUSION: Canine and feline urinary bladder UC represent relevant models of MIBC in humans, and cross-species analysis can identify evolutionarily conserved driver genes. We characterize mutational signatures in bovine UC associated with bracken fern and ptaquiloside exposure, a human-linked cancer exposure. Our work demonstrates the relevance of cross-species comparative analysis in understanding both human and animal UC.	bladder